Communications Biology (Jul 2022)
Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections
- Matthew D. Parker,
- Hazel Stewart,
- Ola M. Shehata,
- Benjamin B. Lindsey,
- Dhruv R. Shah,
- Sharon Hsu,
- Alexander J. Keeley,
- David G. Partridge,
- Shay Leary,
- Alison Cope,
- Amy State,
- Katie Johnson,
- Nasar Ali,
- Rasha Raghei,
- Joe Heffer,
- Nikki Smith,
- Peijun Zhang,
- Marta Gallis,
- Stavroula F. Louka,
- Hailey R. Hornsby,
- Hatoon Alamri,
- Max Whiteley,
- Benjamin H. Foulkes,
- Stella Christou,
- Paige Wolverson,
- Manoj Pohare,
- Samantha E. Hansford,
- Luke R. Green,
- Cariad Evans,
- Mohammad Raza,
- Dennis Wang,
- Andrew E. Firth,
- James R. Edgar,
- Silvana Gaudieri,
- Simon Mallal,
- The COVID-19 Genomics UK (COG-UK) consortium,
- Mark O. Collins,
- Andrew A. Peden,
- Thushan I. de Silva
Affiliations
- Matthew D. Parker
- Sheffield Biomedical Research Centre, The University of Sheffield
- Hazel Stewart
- Department of Pathology, University of Cambridge
- Ola M. Shehata
- Department of Biomedical Science, The University of Sheffield, Western Bank
- Benjamin B. Lindsey
- Sheffield Teaching Hospitals NHS Foundation Trust
- Dhruv R. Shah
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Sharon Hsu
- Sheffield Bioinformatics Core, The University of Sheffield
- Alexander J. Keeley
- Sheffield Teaching Hospitals NHS Foundation Trust
- David G. Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust
- Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University
- Alison Cope
- Sheffield Teaching Hospitals NHS Foundation Trust
- Amy State
- Sheffield Teaching Hospitals NHS Foundation Trust
- Katie Johnson
- Sheffield Teaching Hospitals NHS Foundation Trust
- Nasar Ali
- Sheffield Teaching Hospitals NHS Foundation Trust
- Rasha Raghei
- Sheffield Teaching Hospitals NHS Foundation Trust
- Joe Heffer
- IT Services, The University of Sheffield
- Nikki Smith
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Peijun Zhang
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Marta Gallis
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Stavroula F. Louka
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Hailey R. Hornsby
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Hatoon Alamri
- Department of Biomedical Science, The University of Sheffield, Western Bank
- Max Whiteley
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Benjamin H. Foulkes
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Stella Christou
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Paige Wolverson
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Manoj Pohare
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Samantha E. Hansford
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Luke R. Green
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Cariad Evans
- Sheffield Teaching Hospitals NHS Foundation Trust
- Mohammad Raza
- Sheffield Teaching Hospitals NHS Foundation Trust
- Dennis Wang
- Sheffield Biomedical Research Centre, The University of Sheffield
- Andrew E. Firth
- Department of Pathology, University of Cambridge
- James R. Edgar
- Department of Pathology, University of Cambridge
- Silvana Gaudieri
- Department of Computer Science, The University of Sheffield
- Simon Mallal
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center
- The COVID-19 Genomics UK (COG-UK) consortium
- Mark O. Collins
- Department of Biomedical Science, The University of Sheffield, Western Bank
- Andrew A. Peden
- Department of Biomedical Science, The University of Sheffield, Western Bank
- Thushan I. de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust
- DOI
- https://doi.org/10.1038/s42003-022-03565-9
- Journal volume & issue
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Vol. 5,
no. 1
pp. 1 – 10
Abstract
Matthew Parker et al. use the ARTIC network tiled amplicon PCR and Oxford Nanopore sequencing of thousands of SARS-CoV-2 samples to detect subgenomic RNA changes in the B.1.1.7 lineage endemic in the UK in late 2020/early 2021. They discovered higher subgenomic RNA in B.1.1.7 compared to previous lineages, and find a noncanonical subgenomic RNA that could encode ORF9b.
